User:Tara K. Luckau/Notebook/Team ConGen/Entry Base

From OpenWetWare

< User:Tara K. Luckau | Notebook | Team ConGen(Difference between revisions)
Jump to: navigation, search
Current revision (12:12, 23 May 2013) (view source)
 
(44 intermediate revisions not shown.)
Line 7: Line 7:
<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
<!-- ##### DO NOT edit above this line unless you know what you are doing. ##### -->
__TOC__
__TOC__
-
==27 September 2010 - Ordered Primers==
+
 
-
* Ordered first set of primers
+
 
-
* Scun2 and Scun22 (highly variable simple motifs)
+
==CNTI Acos5==
-
** Lance et al (2009) Conservation Genetics Resources, Sceloporus undulatus
+
 
-
* Forward and reverse as given in publication, also reverse with pigtail (GTTTCTT) at 5' end, also forward with M13F(-21) tag (TGTAAAACGACGGCCAGT)
+
 
-
* [[Image:Luckau_Primer20100927.jpg|500 px]]
+
===PCR===
-
* Try all four combinations
+
 
-
# F - R
+
 
-
# F - R pigtail
+
* comments
-
# F M13 - R
+
:: [[Image:20130110_PCRa.png|800 px]]
-
# F M13 - R pigtail
+
 
-
* If they don't hinder efforts or change optimization decisions, then may make optimization of multiplexes cheaper!
+
 
-
==11 October 2010 - PCR Thermalcycler Testing==
+
===Gel===
-
===Purpose===
+
 
-
* 10μL in each well of full-skirt PCR plate, PCR seal
+
{| {{table}} style="text-align: center"
-
* First set-up of thermalcycler, established User, Protocols, Plates and Masters
+
|-
-
* Data: 20101011_TKL_CyclerTest.tad
+
! Pour !! Load !! Run
-
===Results===
+
|-
-
* Evaporation all around edges
+
| 270 mL 1x TAE + 5.4 g agarose || 2 µL gel load dye + 4 µL PCR product || 160 V
-
* Try using silicone mat?
+
|-
-
===Purpose===
+
| 27 µL GelRed || 6 µL ladder || 45 minutes
-
* 10μL in each well of full-skirt PCR plate, PCR seal, 1 silicone mat
+
|}
-
* Data: 20101011_TKL_CyclerTest1Mat.tad
+
 
-
===Results===
+
 
-
* Still evaporation around edges, but better
+
:: [[Image:20130110_Gela.png|800 px]]
-
* Try using 2 silicone mats?
+
 
-
==12 October 2010 - PCR Thermalcycler Testing==
+
 
-
===Purpose===
+
* mispriming everywhere - primer pair not usable for CNHY
-
* 10μL in each well of full-skirt PCR plate, PCR seal, 2 silicone mats
+
* lots of mispriming, but may be able to use conditions indicated by orange face ([[Image:orangefrownyface.png|20 px]]), if needed, under stringent conditions
-
* Data: 20101012_TKL_CyclerTest2Mat.tad
+
* favorable conditions indicated by [[Image:greenhappyface.png|25 px]]
-
===Results===
+
 
-
* No evaporation!
+
 
-
* Silicone mats got stuck on lid
+
===Fragment Analysis Submission===
-
* Try using 2 silicone mats with tape?
+
 
-
* Try getting samples of different brand of silicone mats, different shape, no holes?
+
 
-
==18 October 2010 - PCR Thermalcycler Testing==
+
* UAGC Submission# ????
-
===Purpose===
+
:: [[Image:20130227_Frag.png|900 px]]
-
* 10µL in each well of full-skirt PCR plate, PCR seal, 2 silicone mats, lab tape on opposite sides
+
 
-
* Data: 20102018_TKL_CyclerTest2MatTape.tad
+
 
-
===Results===
+
* FedEx Tracking# [http://www.fedex.com/Tracking?language=english&cntry_code=us&tracknumbers=801124151779 801124151779]
-
* H6, H7 evaporated, but I think it's workable
+
:: [[Image:20130227_FedEx.png|700 px]]
-
* Plan to do first optimization PCR tomorrow!
+
 
-
==18 October 2010 - Primer Rehydration, Scun2
+
 
-
===Purpose===
+
* FedEx picked up ____pm, 26 February
-
* Rehydrate Scun2 primers for testing tomorrow
+
* FedEx delivered ____am, 27 February
-
# Scun2-F
+
* UAGC received ____am, 27 February
-
# Scun2-R
+
* UAGC completed ____am, 28 February
-
# Scun2-F-M13F(-21)
+
 
-
# Scun2-R-pigtail
+
 
-
===Calculations===
+
 
-
*
+
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->
<!-- ##### DO NOT edit below this line unless you know what you are doing. ##### -->

Current revision

Tara's Lab Notebook Main project page

Contents


CNTI Acos5

PCR

  • comments
Image:20130110 PCRa.png


Gel

Pour Load Run
270 mL 1x TAE + 5.4 g agarose 2 µL gel load dye + 4 µL PCR product 160 V
27 µL GelRed 6 µL ladder 45 minutes


Image:20130110 Gela.png


  • mispriming everywhere - primer pair not usable for CNHY
  • lots of mispriming, but may be able to use conditions indicated by orange face (), if needed, under stringent conditions
  • favorable conditions indicated by


Fragment Analysis Submission

  • UAGC Submission# ????
Image:20130227 Frag.png


Image:20130227 FedEx.png


  • FedEx picked up ____pm, 26 February
  • FedEx delivered ____am, 27 February
  • UAGC received ____am, 27 February
  • UAGC completed ____am, 28 February




Personal tools